Researchers from the Institute of Bioorganic Chemistry, Polish Academy of Sciences (IBCH PAS), working in collaboration with scientists from the University of Ferrara and Poznan University of Medical Sciences, have identified 119 inhibitors of PYCR1, including highly potent compounds with diverse mechanisms of action. Their findings, published in the prestigious Journal of Medicinal Chemistry, reveal new opportunities for targeting an enzyme involved in cancer-associated metabolic reprogramming.

Pyrroline-5-carboxylate reductase 1 (PYCR1) is an enzyme involved in proline biosynthesis that plays an important role in cellular metabolism. Growing evidence links PYCR1 activity to tumor growth, metabolic stress adaptation, and metastasis, making it an emerging target for anticancer drug discovery. However, the development of PYCR1 inhibitors has been hampered by the limited availability of potent chemical compounds and an incomplete understanding of the enzyme’s ligand-binding sites and mechanisms of inhibition.

In their latest study, a research team led by Miłosz Ruszkowski, PhD, DSc, undertook a comprehensive effort to identify novel PYCR1 inhibitors and characterize their molecular mechanisms of action.

From Large-Scale Screening to Novel Inhibitory Mechanisms

The researchers performed high-throughput screening of approximately 100,000 compounds from the European Chemical Biology Library, complemented by a focused collection of kinase inhibitors. This extensive effort resulted in the identification of 119 validated PYCR1 inhibitors representing diverse chemical scaffolds, including several compounds exhibiting submicromolar potency.

A major part of the study involved X-ray crystallography to determine how the identified compounds interact with PYCR1. Remarkably, structural analyses revealed that most characterized ligands bind outside the enzyme’s catalytic site, uncovering several previously underexplored regions suitable for inhibitor development.

Expanding Opportunities for Cancer-Related Drug Discovery

These findings substantially advance our understanding of how PYCR1 can be targeted by small molecules. By revealing new ligand-binding regions and distinct mechanisms of inhibition, the study provides a foundation for the rational development of more potent and selective PYCR1 inhibitors.

The identified compounds also offer valuable starting points for designing molecular probes to investigate the role of PYCR1 in cancer-associated metabolic reprogramming.

Although further optimization and biological validation will be necessary before therapeutic applications can be considered, the findings represent an important advance in establishing PYCR1 as a chemically tractable target.

A Strong Collaborative Effort

The study highlights the strength of interdisciplinary collaboration across research groups within ICHB PAS, combining expertise in structural biology, biochemistry, chemical biology, and enzyme inhibitor discovery.

The project also benefited from close cooperation with researchers at the University of Ferrara (Italy) and Poznan University of Medical Sciences (Poland).

This collaborative effort demonstrates how integrating complementary expertise and experimental approaches can address challenging questions at the interface of molecular biology, medicinal chemistry, and cancer research.

Authors and Funding

The study was authored by Dominika Czerwonka, Wiktoria Ragin-Oh (equal first contributions), Krzysztof Żukowski, Przemysław Piechota, Giuseppe Forlani, Marek K. Bernard, Jacek Łukasz Kolanowski, Dorota Jakubczyk, Dorota Kwiatek-Rożek, and Miłosz Ruszkowski (corresponding author and project leader).

The research was funded by the National Science Centre (Poland) under grant 2021/43/B/NZ7/01611.

Publication:

Czerwonka D., Ragin-Oh W., Żukowski K., et al. Discovery of Potent and Chemically Diverse PYCR1 Inhibitors with Distinct Binding Sites and Modes of Action. Journal of Medicinal Chemistry (2026).

https://doi.org/10.1021/acs.jmedchem.6c02230